A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa
Abstract The Oshima cherry (Cerasus speciosa), which is endemic to Japan, has significant cultural and horticultural value. In this study, we present a near complete telomere-to-telomere genome assembly for C. speciosa, derived from the old growth “Sakurakkabu” tree on Izu Oshima Island. Using Illum...
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Nature Portfolio
2025-02-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-04388-z |
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| author | Kazumichi Fujiwara Atsushi Toyoda Bhim B. Biswa Takushi Kishida Momi Tsuruta Yasukazu Nakamura Noriko Kimura Shoko Kawamoto Yutaka Sato Toshio Katsuki Sakura 100 Genome Consortium Tsuyoshi Koide |
| author_facet | Kazumichi Fujiwara Atsushi Toyoda Bhim B. Biswa Takushi Kishida Momi Tsuruta Yasukazu Nakamura Noriko Kimura Shoko Kawamoto Yutaka Sato Toshio Katsuki Sakura 100 Genome Consortium Tsuyoshi Koide |
| author_sort | Kazumichi Fujiwara |
| collection | DOAJ |
| description | Abstract The Oshima cherry (Cerasus speciosa), which is endemic to Japan, has significant cultural and horticultural value. In this study, we present a near complete telomere-to-telomere genome assembly for C. speciosa, derived from the old growth “Sakurakkabu” tree on Izu Oshima Island. Using Illumina short-read, PacBio long-read, and Hi-C sequencing, we constructed a 269.3 Mbp genome assembly with a contig N50 of 32.0 Mbp. We examined the distribution of repetitive sequences in the assembled genome and identified regions that appeared to be centromeric. Detailed structural analysis of these putative centromeric regions revealed that the centromeric regions of C. speciosa comprised repetitive sequences with monomer lengths of 166 or 167 bp. Comparative genomic analysis with Prunus sensu lato genome revealed structural variations and conserved syntenic regions. This high-quality reference genome provides a crucial tool for studying the genetic diversity and evolutionary history of Cerasus species, facilitating advancements in horticultural research and the preservation of this iconic species. |
| format | Article |
| id | doaj-art-e977a04beb3a4d36a7a83e4118810f37 |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-e977a04beb3a4d36a7a83e4118810f372025-02-09T12:11:23ZengNature PortfolioScientific Data2052-44632025-02-0112111610.1038/s41597-025-04388-zA Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosaKazumichi Fujiwara0Atsushi Toyoda1Bhim B. Biswa2Takushi Kishida3Momi Tsuruta4Yasukazu Nakamura5Noriko Kimura6Shoko Kawamoto7Yutaka Sato8Toshio Katsuki9Sakura 100 Genome ConsortiumTsuyoshi Koide10Mouse Genomics Resource Laboratory, National Institute of GeneticsComparative Genomics Laboratory, National Institute of GeneticsMouse Genomics Resource Laboratory, National Institute of GeneticsCollege of Bioresource Sciences, Nihon UniversityDepartment of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research InstituteGraduate Institute for Advanced Studies, SOKENDAIGenetic Informatics Laboratory, National Institute of GeneticsGraduate Institute for Advanced Studies, SOKENDAIGraduate Institute for Advanced Studies, SOKENDAIKyushu Research Center, Forestry and Forest Products Research InstituteMouse Genomics Resource Laboratory, National Institute of GeneticsAbstract The Oshima cherry (Cerasus speciosa), which is endemic to Japan, has significant cultural and horticultural value. In this study, we present a near complete telomere-to-telomere genome assembly for C. speciosa, derived from the old growth “Sakurakkabu” tree on Izu Oshima Island. Using Illumina short-read, PacBio long-read, and Hi-C sequencing, we constructed a 269.3 Mbp genome assembly with a contig N50 of 32.0 Mbp. We examined the distribution of repetitive sequences in the assembled genome and identified regions that appeared to be centromeric. Detailed structural analysis of these putative centromeric regions revealed that the centromeric regions of C. speciosa comprised repetitive sequences with monomer lengths of 166 or 167 bp. Comparative genomic analysis with Prunus sensu lato genome revealed structural variations and conserved syntenic regions. This high-quality reference genome provides a crucial tool for studying the genetic diversity and evolutionary history of Cerasus species, facilitating advancements in horticultural research and the preservation of this iconic species.https://doi.org/10.1038/s41597-025-04388-z |
| spellingShingle | Kazumichi Fujiwara Atsushi Toyoda Bhim B. Biswa Takushi Kishida Momi Tsuruta Yasukazu Nakamura Noriko Kimura Shoko Kawamoto Yutaka Sato Toshio Katsuki Sakura 100 Genome Consortium Tsuyoshi Koide A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa Scientific Data |
| title | A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa |
| title_full | A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa |
| title_fullStr | A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa |
| title_full_unstemmed | A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa |
| title_short | A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa |
| title_sort | near complete genome assembly of the oshima cherry cerasus speciosa |
| url | https://doi.org/10.1038/s41597-025-04388-z |
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